But army spokesman Brig Gen Fakhrul Ahsan said there were 'several more well-trained operatives active inside the hideout'.
As the operation spills over into the third day, bdnews24.com reports that the army was in for a long haul.
Brig Gen Ahsan confirmed that the operation was far from over and pointed to 'considerable risks' involved in it.
Seventy-eight people trapped inside the building complex were evacuated amid massive firing. While that went on, a blast within a kilometre of the buildings, killed six people including two policemen.
"We're certain that two militants have died. One of them was wearing a suicide vest," said Brig Gen Ahsan. "Our commandos saw them running and fired at them. A suicide blast took place as they fell."
There are still several operatives inside, he said. "They are very alert and are wearing suicide vests."
The building's owner, Ustar Ali, earlier said a couple, Kauser Ali and Morjina Begum, rented a lower-storey flat three months ago.
Home Minister Asaduzzaman Khan Kamal earlier hinted of the possibility that a 'militant leader', maybe inside the Sylhet hideout.
"We cannot say when operation will end," Brig Gen Ahsan told reporters. "Our commandos are trying but it has been difficult."
"The militants have good knowledge on how to fortify a place using bombs."
"We have been applying various tactics since morning … like creating holes using rocket launchers … but those didn’t help much. But when we fired teargas shells, they started running in disarray.
"The reports are simply not correct. We pushed down a wall because it was getting in the way of our firing. Not one tin roof is out of place."
He said no army personnel have been injured in militant assault.
A risky evacuation
The 78 trapped residents were rescued by using a ladder that bridged the rooftops of two buildings because the militants placed IEDs at the entrance and in front of the buildings, said Brig Gen Ahsan.
"Commandos cut the metal grill of a veranda to bring them out. The weather was bad, there was a storm outside. The militants weren't prepared for it."
But an elderly woman who got left behind during the drive on Saturday was later rescued. 'She isn't from Atia Mahal (green building). She is from a nearby white building."
Police's counter-terror unit had led the series of anti-terror operations in the wake of the Jul 1 Gulshan attack in which 22 people were killed.
The army had ended the deadly siege of Holey Artisan Bakery by shooting dead six suspects including five gunmen. It has not taken part in further operations until the raid in Sylhet.
Lt Col Imrul Hasan, commander of the 1st Para-commando Battalion, has been leading the operation.